The Defense Department is setting up its first operational squadron of F-35 Joint Strike Fighter jets, the supersonic stealth aircraft intended to replace at least seven types of military aircraft flown by the United States and its allies.

Despite long-standing turbulence over the program — including sniping over its price tag, time line and ongoing technological development — the Marine Corps on Tuesday will redesignate a Hornet F/A-18 fighter jet squadron in Yuma as Marine Fighter Attack Squadron (VMFA) 121.

The F-35 squadron will be the Pentagon’s first intended to eventually deploy in combat. Its inaugural jet, a B version designed for the Marine Corps to take off on short runways and land vertically like a helicopter, arrived Friday at Marine Corps Air Station Yuma.

The $396 billion F-35 program, the Pentagon’s most expensive and by some measures most ambitious ever, has been under development by Lockheed Martin since 2001. Four years into initial production, the company has been delivering the third lot of Marine B models from its Fort Worth plant this fall.

The aircraft, also called the Lightning II, was conceived as a relatively affordable “fifth generation” stealth jet to be used across the services, saving money through a common production line, design and parts. Three versions were developed: one for the Marine Corps that would protect the service’s ability to operate from short runways in austere locations and small amphibious ships, an Air Force model using conventional runways, and a Navy version for aircraft carriers.

As the Air Force tests and trains on its version and the Navy awaits delivery of its first production tailhook model, the Marine variant has faced the most scrutiny and danger of cancellation.

Former Secretary of Defense Robert Gates put the F-35B on probation, giving developers two years to fix technological and other problems or face cancellation. The B model was cleared from limbo in January, but some lawmakers have continued to press for cancellation to reduce overall F-35 program costs and help balance the federal budget.

With hands-on intervention in the program by the commandant, “we righted that ship,” said Col. Kevin Killea, who oversees aviation requirements for the Marine Corps. Now the growing fleet of trained F-35 pilots and creation of the first operational squadron “tells me the program is progressing forward and meeting the time lines that the Marine Corps needs to transition out of the F/A-18 (Hornet) and the AV-8B (Harrier),” he said. “For me, if it stays on schedule and meets those time lines, it’s more than a success; it’s what we paid for.”

Lockheed Martin officials called the new squadron a significant milestone for the program, showing confidence by the U.S. government in its safety and maturing design.

“These are not test airplanes. These are war-fighting machines that people will train on and become familiar with and ultimately deploy,” said Eric Van Camp, Lockheed manager of F-35 Marine Corps business development.

Lockheed has produced about 65 of the 3,100 F-35 jets in the program of record. The models in operation have flown more than 5,000 hours, a majority of them in the first 10 months of this year, noted Steve O’Bryan, Lockheed’s vice president for F-35 program integration and business development.

The Marines’ short takeoff, vertical landing “B” model is doing particularly well, about 50 percent ahead of its flight test plan this year, he said. “You have an airplane both in production and technical maturity that continues to advance” at an accelerating pace, he said.

Richard Aboulafia, an aviation analyst and vice president for Teal Group, said the F-35 is still “far from ready” to deploy: “In terms of operational capability, it’s extremely limited.” But it is important for Lockheed and the Marine Corps to show the jet in action during development, he added.

“Of all the risks in the program, having a vertical landing model is certainly the most problematic and easily the one most mentioned as a possible budgetary casualty,” Aboulafia said. The Marines also have the most at stake because of their aging fleet of fighter jets and lack of a modern fallback like the Navy and Air Force, he added.

“They need to make this program as firm as possible, both as a form of budgetary protection and to build a bridge from the legacy fleet to the next generation,” Aboulafia said.

By December, the Marine Corps expects to have 17 of its 38 F-35 purchases contracted through 2012, said Capt. Richard Ulsh, a Marine Corps spokesman. Eventually the service hopes to acquire 420 F-35 jets, including 67 of the F-35C carrier version, assigned to 18 active squadrons, two reserve squadrons and two training squadrons.

The first squadron is not expected in San Diego at Marine Corps Air Station Miramar until fiscal 2021. The Navy expects to receive its first production jet in February, at Eglin Air Force Base, Fla., as it establishes the first F-35C training squadron.

Meanwhile, the military has been prepping pilots at the F-35 Integrated Training Center at Eglin and testing the aircraft at Edwards Air Force Base, Naval Air Station Patuxent River, Md., and at sea.

The new Yuma squadron has long been in the works. Lt. Col. Jeff Scott, commanding officer of VMFA-121, was selected for the job two years ago. The Harrier pilot and two-time Iraq combat veteran finished his F-35 conversion training at Eglin last week.

“It’s an amazing airplane, it flies extremely well. It is not just the next step in aircraft, it is five or six steps beyond what we currently have. It is growing into those capabilities in terms of the software and (flight) testing,” Scott said, but compared with the Corps’ current vertical landing jet — the Harrier introduced in the ’80s — it is faster, more stable, more maneuverable and easier to fly because of computerized flight controls.

“The integrated sensors of the aircraft are extremely impressive. The computer does a lot of the work. The computer sorts out a lot of things and gives the pilots a lot of information,” Scott said.

The squadron has about half of the 300 personnel it needs and four pilots qualified to fly the 16 jets that will eventually be assigned to the unit. It is also the first to have its own maintenance crews currently training to service the aircraft, instead of relying on Lockheed contractors.

The squadron hopes to be cleared by the 3rd Marine Aircraft Wing and the Commander of Naval Air Forces to fly around Yuma by late December or early January, pending inspection of its maintenance and other processes.

Tactical training may begin within a year after 10 to 12 pilots are qualified to fly. But the squadron won’t be able to deploy until it has jets with block 2B software revisions, which Lockheed said it expects to deliver in mid-2015.

Currently only F-35 test pilots are allowed to operate the F-35B’s signature feature in flight — its ability to land vertically. That should change for the Yuma pilots within a year, said Maj. Aric Liberman, a former Navy SEAL turned Hornet pilot who will be the aviation maintenance officer for VMFA-121.

Liberman has been stationed at Eglin for more than three years, training on the F-35 mostly on simulators. He took his first flight in the new jet in August.

After powering up and rolling down the runway, his 40-minute midmorning cruise over the Gulf of Mexico was “business as usual,” he recalled. “It was the most exciting nonevent I’ve ever done in my life, because the jet is so easy to fly and because I had so much preparation.”

Flying the F-35 that first time was similar to flying a Hornet, except for the helmet-mounted display, touch-screen controls on the glass cockpit, and the added thrill that “it’s a new aircraft and you’re on the edge of Marine Corps aviation.”

It seemed like a slow start getting the program off the ground. Now the squadron will have a lot of work and learning to do in coming years to help the Marine Corps integrate the F-35 into its operations, Liberman said.

“We’ve really gained a lot of momentum,” he said. “I am excited to make that transition. That is what we are here to do — to learn how to employ the aircraft as a weapon system.”